RNA interference (RNAi) is an evolutionarily conserved, homology-based gene silencing mechanism, in which small interfering RNAs (siRNAs) lead to mRNA degradation and/or heterochromatin formation in host cells. This molecular pathway is fundamentally important for development transition and cellular responses to pathogenic challenges. The siRNA-mediated heterochromatic response, which is referred to as nuclear RNAi in this proposal, has been of great interest as an epigenetic mechanism by which events at the RNA level can feed back to modulate chromatin structure and function. The most exciting aspect of this phenomenon is its remarkable ability to transmit epigenetic information through mitotic or meiotic cell cycles. This was best studied in RNA-mediated DNA methylation in plants and RNA-mediated transcriptional silencing in fission yeast. However, the extent to which this process can lead to a trans-generational response in animals remains largely unknown. The most definitive evidence came from the study of germline nuclear RNAi in C. elegans. Although related studies in mammals are far from conclusive, both the heterochromatin response and many of the C. elegans RNAi components can be found in humans as well. Defining molecular details of the germline nuclear RNAi pathway in a highly tractable model organism C. elegans will provide important insights into conserved mechanisms of chromatin-based genome regulation and epigenetic inheritance. The following fundamental questions in this model must be experimentally addressed for the field to move forward. What are the natural targets of germline nuclear RNAi? How are transcription and silencing of target genes coordinated during germline development? What are the mechanisms of epigenetic inheritance that maintain the silencing of target genes in successive reproductive cycles? Addressing these fundamental questions will help us to predict the sensitivity of a chromatin locus to a targeting regulatory RNA, which is critically important to our long-term goal of targete chromatin intervention as a therapeutic tool. We will employ a combination of experimental and computational approaches to address these questions in three specific aims: (1) Genome-wide identification, characterization, and classification of nuclear RNAi targets in the C. elegans germline. (2) Determine the role of promoters in regulating germline nuclear RNAi. (3) Determine the role of heterochromatin in trans- generational gene silencing mediated by germline nuclear RNAi. The proposed studies, which probe fundamental yet uncharted areas, will hold profound implications for understanding of genome-environment interaction and inheritance of expression states relevant to human development and disease.